Got the solution
when I tried to click on the button a second time alert Keywords were able to identify the alert.
so I implemented the following to handle it
WebUI.click(findTestObject('Web/Sales Order Upload/Upload Data button'))
try { WebUI.delay(2)
WebUI.verifyAlertPresent(1)
}
catch(Exception ex) {
WebUI.switchToDefaultContent()
WebUI.click(findTestObject('Web/Sales Order Upload/Upload Data button'))
}